A metadata is a piece of data used to define or describe another piece of data. In the case of a genome, the data is the sequence(s) and the metadata can describe the shape of the cell, its motility, the temperature at which it grows best, the known metabolic pathways, etc.

This page presents the metadata available in MicroScope. Those metadata can be used in the Advanced Selector to select objects. Note that we only support qualitative metadata for now.

Species metadata

Currently, there is only one source of metadata associated to the species of the genome (identified by its NCBI taxid).

Source of data

Species metadata are taken from Joshua S. Madin et al., A synthesis of bacterial and archaeal phenotypic trait data. Sci Data 7, 170 (2020). This article unifies phenotypic and quantitative genomic traits from 26 sources. The description of all available data can be seen here. We use version 1.2.


For our use, we have selected 9 qualitative metadata which are described in the table below:

Selected metadata in MicroScope

Trait name


Exemple values

Cell shape

The typical shape of cells

bacillus, coccobacilus, …

Gram stain

Gram positive or negative

Gram positive, Gram negative


Capacity to move

motile/non motile, gliding, …


Can produce spores

sporulating/non sporulation


Oxygen usage

aerobic, microaerophilic, …

Range tmp

Coarse environmental preference

mesophilic, psychrophilic, …

Range salinity

Coarse environmental preference

stenohaline, halophilic, euryhaline, …


List of metabolic pathways undertaken

aerobic_anoxygenic_phototrophy, fermentation, nitrate_reduction, …

Isolation source

Where the microbe was sourced from

host, biofilm, soil, …

See the reference for more precise description and the meaning of the values.